N - mixture models by species
modelling N by site to get relative abundance
abundance by site will be used as a cov on predator occupancy
7 models evaluated, dot, jdt + jdtSQ, lure + jdt + jdtSQ
Species: Â Â Â Â BeldingsGroundSquirrel
Detections by Year:
|
Yr
|
2016
|
2017
|
2018
|
2019
|
2020
|
|
sites
|
19
|
31
|
19
|
32
|
26
|
|
detections
|
10
|
56
|
3
|
0
|
3
|
|
N.dot.model
|
5
|
16
|
2
|
0
|
2
|
WAIC
Models by WAIC:
|
model
|
description
|
WAIC
|
N.total.est
|
|
fm7
|
counts
|
13.94475
|
54
|
|
fm5
|
jdt + jdtSq
|
315.37097
|
39
|
|
fm6
|
lure + jdt + jdtSq
|
316.37138
|
39
|
|
fm2
|
jdt
|
324.57210
|
38
|
|
fm4
|
lure + jdt
|
326.28625
|
39
|
|
fm1
|
dot
|
423.41197
|
25
|
|
fm3
|
lure
|
427.11536
|
30
|
Model summaries:
model: fm1
summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
p[1]
|
NA
|
6209
|
0.097
|
0.084
|
0.04
|
0.16
|
0
|
1.0008
|
|
p[2]
|
NA
|
5130
|
0.130
|
0.129
|
0.09
|
0.17
|
0
|
1.001
|
|
p[3]
|
NA
|
4800
|
0.039
|
0.023
|
0.00
|
0.07
|
0
|
0.994
|
|
p[4]
|
NA
|
9978
|
0.483
|
0.142
|
0.00
|
0.88
|
0
|
0.9829
|
|
p[5]
|
NA
|
4589
|
0.034
|
0.021
|
0.00
|
0.06
|
0
|
0.9931
|
|
lambda[1]
|
NA
|
3566
|
0.318
|
0.221
|
0.07
|
0.54
|
0
|
1.0006
|
|
lambda[2]
|
NA
|
6793
|
0.637
|
0.583
|
0.33
|
0.92
|
0
|
1.001
|
|
lambda[3]
|
NA
|
1613
|
0.224
|
0.068
|
0.00
|
0.41
|
0
|
0.9871
|
|
lambda[4]
|
NA
|
7897
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
lambda[5]
|
NA
|
1599
|
0.201
|
0.057
|
0.00
|
0.39
|
0
|
0.988
|
|
N[68]
|
NA
|
2494
|
0.112
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[119]
|
NA
|
3596
|
0.144
|
err
|
0.00
|
1.00
|
err
|
err
|
|
N[37]
|
NA
|
8671
|
1.055
|
err
|
1.00
|
1.00
|
err
|
err
|
|
N[9]
|
NA
|
4296
|
0.072
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[81]
|
NA
|
0
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
p[1]

p[2]

p[3]

p[4]

p[5]

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[68]

N[119]

N[37]

N[9]

N[81]
## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha
|
jdt
|
2005
|
2.069
|
2.075
|
1.60
|
2.51
|
0
|
1.001
|
|
alpha0
|
NA
|
1890
|
-3.991
|
-3.949
|
-4.54
|
-3.38
|
0
|
1.001
|
|
lambda[1]
|
NA
|
8461
|
0.326
|
0.23
|
0.08
|
0.54
|
0
|
1.0008
|
|
lambda[2]
|
NA
|
8231
|
0.969
|
0.866
|
0.55
|
1.37
|
0
|
1.001
|
|
lambda[3]
|
NA
|
9042
|
0.145
|
0.076
|
0.00
|
0.28
|
0
|
0.9939
|
|
lambda[4]
|
NA
|
10000
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
lambda[5]
|
NA
|
10000
|
0.116
|
0.05
|
0.01
|
0.22
|
0
|
0.9939
|
|
N[38]
|
NA
|
9522
|
0.913
|
0
|
0.00
|
2.00
|
1
|
err
|
|
N[68]
|
NA
|
7712
|
0.034
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[16]
|
NA
|
9610
|
0.075
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[91]
|
NA
|
0
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[15]
|
NA
|
10000
|
0.056
|
err
|
0.00
|
0.00
|
err
|
err
|
alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[38]

N[68]

N[16]

N[91]
## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[15]

alpha relationship

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha
|
lure
|
9106
|
0.179
|
0.196
|
-0.04
|
0.41
|
0.42161
|
0.8983
|
|
alpha0
|
NA
|
4026
|
-2.477
|
-2.423
|
-2.83
|
-2.12
|
0
|
1.001
|
|
lambda[1]
|
NA
|
8326
|
0.346
|
0.255
|
0.09
|
0.58
|
0
|
1.0008
|
|
lambda[2]
|
NA
|
5292
|
0.986
|
0.908
|
0.52
|
1.41
|
0
|
1.001
|
|
lambda[3]
|
NA
|
10000
|
0.116
|
0.056
|
0.01
|
0.22
|
0
|
0.9939
|
|
lambda[4]
|
NA
|
10000
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
lambda[5]
|
NA
|
10000
|
0.091
|
0.046
|
0.00
|
0.17
|
0
|
0.9935
|
|
N[55]
|
NA
|
10000
|
0.005
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[68]
|
NA
|
9844
|
0.008
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[106]
|
NA
|
10000
|
0.065
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[50]
|
NA
|
8965
|
0.043
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[116]
|
NA
|
9698
|
0.032
|
err
|
0.00
|
0.00
|
err
|
err
|
alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[55]

N[68]

N[106]

N[50]

N[116]

alpha relationship

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha[1]
|
lureDays
|
6764
|
-0.074
|
-0.096
|
-0.34
|
0.20
|
0.85684
|
0.6755
|
|
alpha[2]
|
julianDt
|
2000
|
2.073
|
2.051
|
1.62
|
2.50
|
0
|
1.001
|
|
alpha0
|
NA
|
1764
|
-4.019
|
-3.977
|
-4.60
|
-3.44
|
0
|
1.001
|
|
lambda[1]
|
NA
|
8807
|
0.323
|
0.236
|
0.08
|
0.55
|
0
|
1.0009
|
|
lambda[2]
|
NA
|
8112
|
0.987
|
0.95
|
0.55
|
1.39
|
0
|
1.001
|
|
lambda[3]
|
NA
|
10000
|
0.146
|
0.065
|
0.00
|
0.28
|
0
|
0.9938
|
|
lambda[4]
|
NA
|
10000
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
lambda[5]
|
NA
|
8183
|
0.130
|
0.054
|
0.00
|
0.25
|
0
|
0.9936
|
|
N[81]
|
NA
|
0
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[59]
|
NA
|
9292
|
0.037
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[30]
|
NA
|
10000
|
1.036
|
err
|
1.00
|
1.00
|
err
|
err
|
|
N[56]
|
NA
|
10000
|
0.032
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[13]
|
NA
|
9707
|
1.053
|
err
|
1.00
|
1.00
|
err
|
err
|
alpha[1]

alpha[2]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[81]
## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[59]

N[30]

N[56]

N[13]

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha[1]
|
julianDt
|
66
|
5.611
|
5.04
|
3.25
|
8.22
|
0
|
1.001
|
|
alpha[2]
|
julianDtSq
|
72
|
-1.779
|
-1.598
|
-2.92
|
-0.66
|
0.02373
|
0.9992
|
|
alpha0
|
NA
|
73
|
-5.853
|
-5.551
|
-7.37
|
-4.24
|
0
|
1.001
|
|
lambda[1]
|
NA
|
9585
|
0.313
|
0.241
|
0.08
|
0.53
|
0
|
1.0008
|
|
lambda[2]
|
NA
|
6519
|
1.067
|
0.95
|
0.58
|
1.54
|
0
|
1.001
|
|
lambda[3]
|
NA
|
10238
|
0.142
|
0.076
|
0.00
|
0.27
|
0
|
0.9927
|
|
lambda[4]
|
NA
|
10000
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
lambda[5]
|
NA
|
9414
|
0.114
|
0.063
|
0.00
|
0.22
|
0
|
0.9934
|
|
N[125]
|
NA
|
10595
|
0.114
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[72]
|
NA
|
0
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[127]
|
NA
|
10000
|
0.035
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[4]
|
NA
|
10291
|
1.056
|
err
|
1.00
|
1.00
|
err
|
err
|
|
N[93]
|
NA
|
0
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
alpha[1]

alpha[2]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[125]

N[72]
## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[127]

N[4]

N[93]
## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

julian date relationship

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha[1]
|
lureDays
|
5902
|
-0.023
|
-0.026
|
-0.30
|
0.24
|
0.98436
|
0.5595
|
|
alpha[2]
|
julianDt
|
96
|
5.479
|
5.022
|
3.34
|
7.72
|
0
|
1.001
|
|
alpha[3]
|
julianDtSq
|
106
|
-1.715
|
-1.595
|
-2.70
|
-0.69
|
0.0067
|
1.0002
|
|
alpha0
|
NA
|
101
|
-5.785
|
-5.712
|
-7.16
|
-4.43
|
0
|
1.001
|
|
lambda[1]
|
NA
|
8592
|
0.311
|
0.229
|
0.08
|
0.52
|
0
|
1.0009
|
|
lambda[2]
|
NA
|
6730
|
1.064
|
0.944
|
0.58
|
1.52
|
0
|
1.001
|
|
lambda[3]
|
NA
|
9665
|
0.144
|
0.066
|
0.01
|
0.28
|
0
|
0.9935
|
|
lambda[4]
|
NA
|
10000
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
lambda[5]
|
NA
|
7892
|
0.121
|
0.056
|
0.01
|
0.23
|
0
|
0.9937
|
|
N[118]
|
NA
|
8579
|
0.032
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[97]
|
NA
|
0
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[40]
|
NA
|
8481
|
0.100
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[36]
|
NA
|
9554
|
1.166
|
err
|
1.00
|
2.00
|
err
|
err
|
|
N[69]
|
NA
|
10000
|
0.033
|
err
|
0.00
|
0.00
|
err
|
err
|
alpha[1]

alpha[2]

alpha[3]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[118]

N[97]
## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[40]

N[36]

N[69]

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha
|
counts
|
7690
|
13.312
|
13.448
|
11.04
|
15.57
|
0
|
1.001
|
|
alpha0
|
NA
|
6710
|
-5.721
|
-5.525
|
-6.71
|
-4.67
|
0
|
1.001
|
|
lambda[1]
|
NA
|
7367
|
0.916
|
0.667
|
0.24
|
1.59
|
0
|
1.0007
|
|
lambda[2]
|
NA
|
9657
|
0.984
|
0.933
|
0.55
|
1.39
|
0
|
1.001
|
|
lambda[3]
|
NA
|
4586
|
0.765
|
0.367
|
0.04
|
1.47
|
0
|
0.9928
|
|
lambda[4]
|
NA
|
4640
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
lambda[5]
|
NA
|
3342
|
0.737
|
0.396
|
0.04
|
1.43
|
0
|
0.9921
|
|
N[54]
|
NA
|
7143
|
0.738
|
0
|
0.00
|
2.00
|
1
|
err
|
|
N[89]
|
NA
|
10000
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[97]
|
NA
|
10000
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[22]
|
NA
|
0
|
1.000
|
err
|
1.00
|
1.00
|
err
|
err
|
|
N[60]
|
NA
|
7190
|
0.727
|
0
|
0.00
|
2.00
|
1
|
err
|
alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[54]

N[89]

N[97]

N[22]
## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[60]

alpha relationship
